The whole idea that animals are lesser and inferior has caused so many problems in our society. In the religous community, animals have no souls, so not only can you treat them atrociously, but if you can put a group or race or gender in the category of being merely animals, you can justify all sorts of brutality and oppression also.
Some scientists share the same view of animals, that they are brutish and have no ethics or morality, so if human beings are just another animal, you can justify brutish and violent acts of humans towards other humans.
I don’t think the belief animals have no soul is a particularly religious belief. I would say it is prevalent in secular society as well, as you have suggested with your statement about scientists.
The “animals have no soul” rationalization gives humans credence to use them as property and objects for material gain. A similar argument toward people of color and the justification for slavery used in the past was once prevalent.
Whether animals have souls or not is actually irrelevant. No one knows if humans have souls either. It is only an assumption and belief that makes humans feel superior over other animals. What we all have, instead, is sentience. The ability to feel pain and awareness, and is much more measurable. Thus, sentience holds a higher standard to ethics towards animals than any religious belief about them ever has.
Not surprisingly, the Bible has a lot of contradictions about animals. In the beginning god made us all vegetarians. Well that didn’t last long. As typical, theologians and Christians pick and choose the parts of the Bible to accentuate and hold close to their hearts. Those choices tend to work against any benefit to animals. If we all followed certain beliefs about animals in the Bible that do not encourage the “dominion” beliefs about our relationship to them, we would not have a history of treating them as atrociously as you pointed out. Likewise, if we all followed Jesus’ beliefs about peace and social justice, our treatment towards humans would have vastly improved as well.
But I’m not a bible thumper so I’m not arguing for an increase in bible reading. My point is that religion and the bible in particular are so arbitrary and contradictory that you can justify just about anything if you look hard enough.